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{{Coexpression_clusters
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|full_id=C4700_thymus_adrenal_Whole_acute_CD4_Burkitt_Reticulocytes
|id=C4700
|ontology_enrichment_celltype=CL:0000542!9.07e-20!53;CL:0000051!9.07e-20!53;CL:0000838!3.16e-19!52;CL:0000084!4.19e-11!25;CL:0000827!4.19e-11!25;CL:0000791!2.25e-09!18;CL:0000789!2.25e-09!18;CL:0002420!2.25e-09!18;CL:0002419!2.25e-09!18;CL:0000790!2.25e-09!18;CL:0000945!2.28e-08!24;CL:0000826!2.28e-08!24;CL:0000625!8.58e-08!11;CL:0000988!7.45e-07!182
|ontology_enrichment_disease=DOID:2531!1.10e-10!51;DOID:0060083!1.10e-10!51;DOID:1240!3.42e-09!39;DOID:8692!3.13e-08!31;DOID:0050686!1.50e-07!137
|ontology_enrichment_uberon=UBERON:0000178!2.40e-09!15;UBERON:0000179!2.40e-09!15;UBERON:0000463!2.40e-09!15
}}

Latest revision as of 14:18, 17 September 2013


Full id: C4700_thymus_adrenal_Whole_acute_CD4_Burkitt_Reticulocytes



Phase1 CAGE Peaks

Hg19::chr7:75932863..75932900,+p4@HSPB1
Hg19::chr7:75932909..75932923,+p6@HSPB1
Hg19::chr7:75932929..75932953,+p5@HSPB1


Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data

No results for this coexpression

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data

No GOStat results

Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br>cell_data<br>uberon_data<br>disease_data<br>

Uber Anatomy
Ontology termp-valuen
blood1.65e-0915
haemolymphatic fluid1.65e-0915
organism substance1.65e-0915
Disease
Ontology termp-valuen
hematologic cancer5.59e-1051
immune system cancer5.59e-1051
leukemia2.41e-0839
organ system cancer3.36e-08137
myeloid leukemia2.38e-0731


Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data

Novel motifs



JASPAR motifs

Motifs-log10(p-value)
MA0003.10.178364
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.11.24048
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.11.58389
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.10.94098
MA0040.11.24388
MA0041.11.97353
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.10.904546
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.14.06645
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.11.04561
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.110.4901
MA0074.10.935474
MA0076.11.74184
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.257905
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.11.55947
MA0103.10.628063
MA0105.14.18141
MA0106.10.986396
MA0107.14.63461
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.10.560723
MA0117.11.36676
MA0119.16.82664
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.10.440097
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.273764
MA0146.10.348055
MA0147.10.565108
MA0148.13.29283
MA0149.10.884158
MA0062.21.141
MA0035.22.07011
MA0039.20.757898
MA0138.21.04628
MA0002.21.20011
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.264678
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.711948
MA0156.11.60572
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.12.05956
MA0163.10.776149
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.25.16052
MA0102.21.88331
MA0258.10.519674
MA0259.11.40979
MA0442.10



ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
CCNT2#90536.336201576962630.003930750035764890.0191136792525025
CHD2#1106310.34402283411690.0009033701102746880.00662828937382171
CTBP2#1488362.71700033932814.049570681927e-060.000130575212241363
E2F1#186934.907389214879320.008460985347239390.0327729425019595
E2F6#187635.017155731697390.00791769806886330.0324293685483358
EGR1#195834.988179094810140.008056488137383440.0322466395040888
ELF1#199734.258097958807540.01295179875054610.0464947894582299
ELK4#2005316.2356816584680.0002336043955745990.00256409978659123
EP300#203336.77394172622320.003216880500103790.0168506260683288
ETS1#211339.728760922202340.001085840092584840.00765261174367148
GABPB1#255337.067683836182170.002832212825417420.0154817060229127
GATA1#2623313.56030814380040.0004009615963782630.0038947198813383
HMGN3#932438.178547723350590.001827766942164210.0109204892261263
IRF1#365937.63716375356390.002244692747297240.0128731791683585
JUND#372736.994663941871030.002921845042734990.0157686324110273
MAX#414936.452555509007120.003721913834265510.0187430907438572
MXI1#460139.96157162875930.001011470541259020.00723491348938778
MYC#460935.22228187160940.007020843755740150.0296071186709903
NANOG#79923329.24477848101273.99627955670032e-050.000741327603236634
NFKB1#479035.488063424193840.006049381815655430.0270841251530517
NR3C1#2908314.9730233311730.0002978331194675480.00310278236050586
NRF1#4899312.21027944771090.0005492172401020010.00473460167882896
REST#597839.650028716128020.001112636247114590.0077134163300631
SIN3A#2594235.408884726815140.006318961977991520.0278270395521781
SP1#666735.69838137814090.005403962701712170.024788495283034
STAT3#6774310.51946499715420.0008589184530415310.00645588947946775
TAL1#6886329.86861667744023.75103522793067e-050.000722794037213747
YY1#752834.911170749853860.008441455341808260.033124822635473
ZBTB7A#5134137.35190930787590.002516255860282270.0140908978976954
ZNF263#1012738.221841637010680.001799043925565870.011013502259213



Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data

This analysis result is provided for C0 - C305 clusters.

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